chr7-49417471-A-G

Variant names:

• chr7-49417471-A-G
• rs13228770

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.369 in 151,900 control chromosomes in the GnomAD database, including 11,357 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (11357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56027 AN: 151782 Hom.: 11351 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.390

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 56047 AN: 151900 Hom.: 11357 Cov.: 32 AF XY: 0.369 AC XY: 27364 AN XY: 74200

African (AFR) AF: 0.210 AC: 8727 AN: 41474

American (AMR) AF: 0.327 AC: 4988 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2889 AN: 5142

South Asian (SAS) AF: 0.339 AC: 1629 AN: 4810

European-Finnish (FIN) AF: 0.411 AC: 4323 AN: 10522

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30357 AN: 67930

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.280 Hom.: 1346

Bravo AF: 0.360

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.61
PhyloP100		-0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13228770; hg19: chr7-49457067;